I suspect the issue is that the columns in both tables have the same names. Therefore, JMP will overwrite the values. Here is a simple example on how I would handle this. Now, given this type of Update, the two data tables will be lined up, row 1 with row 1.
That may result in the issue that you can not compare across columns, since the relationship between them does not exist.
dt << Row Selection( Select where( (:Freq == "F0"), Current Selection( Extend )) );
dt << Select Columns( [15,19] );
dt2 = dt << Subset( ( Selected Columns ), Output Table Name( "F0" ) );
dt << clear select;
dt << Row Selection( Select where( (:Freq == "F1"), Current Selection( Extend )) );
dt << Select Columns( [15,19] );
dt3 = dt << Subset( ( Selected Columns ), Output Table Name( "F1" ) );
// Rename the columns
column(dt3,1) <<set name((column(dt3,1) << get name) || " 2");
column(dt3,2) <<set name((column(dt3,2) << get name) || " 2");
// Merge the data tables
dt2 << update(with(dt3));
Jim